Ok, just booted up the game to work on this and...what you are seeing is not my bug. On my screen the model is (mostly) centered inside of the black box. So the fact that it is shifted so far up in your screenshot has to be a mod conflict with some other mod you are using that is changing the base-game's artwork for the chemical plant.
Also, the reason I put the black box there was because the model for the chem plant is not symmetrical / square, so when you rotate it to the side it is too small for the box left-to-right, but if I made it any bigger to fix that the fluid inputs would be asymmetric and look weird. So..sorry, but without completely re-modeling a chem plant in Blender (If you think I have the skill to do that, check out my Nuclear Rebalance mod... the models in that mod are the limit of my Blender skill) I can't fix it.
As for how the 'where' part of the fluid inputs are determined: Fluid inputs will always start with one input directly in-line with the visual model. Then the others will be spaced nearby 3 units apart (so that you can use a storage tank + pump to get full throughput -- technically I should lower the value to be 7200 u/s from 12k because the base-game pumps haven't been able to move 12k/s since 0.17 due to backend fluid changes. The devs know about this and have no plans to fix it. I use a customized version of the 'compressed fluids' mod that I haven't shared anywhere so that I can get around this issue and actually move 12k/s. Anyway, yea, the additional inputs are spaced out, left, then right, of the 'starting point' until enough inputs exist to handle the flow the building needs. Let me try some ASCII art to explain how it works:
'
|-1-i-2--i-1-|
| |
| |
| |
|-1-o-----o--|
'
So your browser probably won't use a monospace font for that. Copy-paste it into notepad or some other thing where you can view it with a monospace font like courier and it will look right. In the above image, the inputs need 5 total inputs to match building inflow needs, so additional inputs 1 (2x of these) and 2 (1x of these) are created to the left and right of the 'starting' inputs. On the output side, 1 additional input is needed (the '1') is placed to the side of one of the outputs.
Factorio's website is trimming away all of my ascii spaces, so...use your imagination I guess. :( I tried.